|
| Status |
Public on Nov 21, 2012 |
| Title |
2',3'-cyclic phosphate-terminated RNA, Ski2Δ +DTT Technical Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Ski2Δ +DTT
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: Ski2-delta
stress: stress (+DTT)
|
| Treatment protocol |
Samples were taken after treatment with 2mM DTT for 1 hour.
|
| Growth protocol |
Cells were cultured in YE5S media (rich media). Samples were taken from mid-log growing cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphates in total RNA. Deep-sequencing libraries were constructed as described in Ingolia et al, 2011. To capture 2',3'cyclic-phosphate 3' ends the libraries were constructed according to Schutz et al., 2010.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2',3'-cyclic phosphate-terminated RNA
|
| Data processing |
Basecalls performed using CASAVA version 1.4
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S. pombe rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the none-rRNA and none-tRNA reads were aligned against the S. pombe genomic sequences.
reads with no alignment against S. pombe genomics sequences were re-aligned against the library of pombe processed protein-coding transcripts.
Genome_build: Recent genome build (09/05/2011) from the PomBase
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Aug 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Philipp Kimmig |
| Organization name |
University of California, San Francisco
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Peter Walter lab
|
| Street address |
Genentech Hall N316, 600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-2517 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE40298 |
The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis |
|
| Relations |
| SRA |
SRX180550 |
| BioSample |
SAMN01121956 |
